Access Data & Specimens

Accessing PPMI Data & Specimens

A primary goal of PPMI is to develop a large and comprehensive set of correlated clinical data and biospecimens that will be made available to the entire scientific community to help accelerate biomarker verification research. This section of the study site serves as the central hub for academic and industry researchers to download de-identified data and request specimens collected in the study.

PPMI data and specimens have been collected in a standardized manner under strict protocols developed by the steering committee. Click here to review the PPMI Research Documents and SOPs that have been developed to guide PPMI Clinical Sites in data and specimen collection.

PPMI Data: Clinical, Biomarker, Imaging and Related MetaData

The PPMI study dataset includes clinical, biological and imaging data collected at PPMI clinical sites. The data have been aggregated into the PPMI study database, which is managed by the PPMI Bioinformatics Core, the Laboratory of NeuroImaging (LONI) at the University of Southern California.

PPMI Data: Raw Whole Exome and Genome Sequencing Data

Whole exome and genome sequencing were performed on whole-blood extracted DNA samples (details may be found in the Exome Sequencing and Genome Sequencing Methods documents available in the Genetic Data Download section of the PPMI database). Genomic VCF (gVCF) data files generated from the exome and genome sequencing processes are currently available for download by authorized PPMI investigators from within the PPMI database. PPMI also makes available the raw data files. However, due to the size of these files, they cannot be reasonably distributed over the Internet. Investigators interested in obtaining data in BAM and/or FASTQ format may submit a request for these data to be shipped on sets of loaner external drives. Note: Whole Exome Sequencing BAM files will require approximately 15TB of disk space and FASTQ files 130 GB of disk space. Whole Genome Sequencing FASTQ files will require approximately 70 TB of disk space.

Investigators requesting FASTQ and/or BAM files must have an active PPMI database account and submit a PPMI Whole Exome Sequencing Data Agreement, and/or PPMI Whole Genome Sequencing Data Agreement to ppmi@loni.usc.edu. These forms are available in the Genetic Data Download section of the PPMI database. Data requests will be filled in the order received. LONI will contact you when the hardware becomes available to verify shipping information. The hardware must be returned within 3 weeks of receipt.

PPMI Samples: Biologic Specimens

Biologic specimens collected through PPMI include urine, plasma, serum, cerebrospinal fluid, DNA and RNA. An inventory of collected specimens available for research purposes is available in the PPMI study database. Researchers may apply for access to stored samples, which are housed in the study’s biorepositories in the US, Italy and Israel.

PPMI Samples: Cell Lines

Fibroblasts and iPSCs were generated from skin biopsies from 20 PD subjects and 5 healthy controls at one US PPMI site through a pilot sub-study with the New York Stem Cell Foundation (NYSCF). In 2016, PPMI expanded to generate iPSCS from blood-based collection from a subset of US sites through the Golub Capital iPSC PPMI Sub-study with Cellular Dynamics International (CDI). The sub-study with CDI aims to collect blood for iPSC generation from PPMI subjects across all study arms. Researchers may apply for access to stored cell lines, which are housed in the study’s biorepository at Indiana University.

Analysis of PPMI Data and Samples

The PPMI Steering Committee has already identified preliminary analyses that will be conducted on the PPMI data by the study cores. Other investigators are strongly encouraged to access the study data and specimens to conduct their own analyses. To keep the scientific community apprised of analyses being completed by all investigators who are using PPMI data and specimens. A list of Ongoing Analyses has been compiled here.